Demonstration of a Universal Surface DNA Computer August 3, 2004 Summarized by Ji-Yoon Park Xingping Su and Lloyd M. Smith* Nucleic Acids Res. 32, (2004)

Abstract  Concept of universal Turing machine  Abstract definition of a general purpose computer  General purpose (universal) computer  can compute anything that is computable  any computer can simulate Boolean logic circuits of any complexity  Simulating Boolean logic circuits  The NOR gate: universal gate in Boolean logic gate  Any other logic gate can be built from it alone  Universal nature of surface DNA computing model

Computational Complexity (1/2)  In computational complexity theory  the class of NP-complete  A subset of the universal class  Boneh et al. (1996): theoretically solve beyond NP class  Winfree (2000): self assembly/ theoretically & experimentally  Benenson et al. (2001): only read/ less powerful than universal TM  Stojanovic & Stefanovic (2003) : deoxyribozyme-based logic gated & automata/ non-universality  Smith group’s work  Liu et al. (2000): surface-based computer  Frutos et al. (1997): multiple-word encoding  Cai et al. (1997): surface DNA computing model for Boolean logic circuits  In this paper…  Surface DNA computing model to simulate a Boolean logic circuits

 P-complete - a set of decision problemsdecision problems - useful in the analysis of which problems can be efficiently solved on parallel computers Computational Complexity (2/2)

NOR gate is “universal” – Continuous input

Sequences of the DNA encoding

Word & Word Complement

Experimental Section 1. Sequence design of DNAs and DNA/LNA chimeras 2. DNA attachment 3. Melting analysis 4. Hybridization/ Ligation/ Polymerase extension 5. Efficiency of ligase & computation

X1=F, X2=F, X3(X)= T or F X1, X2 Complements & hybridization LigationMelting Polymerase extension X4=T X1=T, X2=T complements & hybridization & extension Ligation X4=F After NOR gate computation After OR gate computation X3=F, X4=F NOT gate Continuous input

NOR gate is “universal” – Non-continuous input

X1=T, X3=T complements of LNA/DNA chimera Polymerase extension & X4=T X1=T, X3=T complements of regular DNA X4=F, Polymerase extension NOR gate computation MARK Operation of OR gate After OR gate computation Non-continuous input

Circuit Computations After NOR gate FT complement to X4=T After OR gate FT complement to X5=T After NOR gate FT complement to X5=F After NOR gate FT complement to X4=F

Overall Computation Efficiency

Sequence design of DNAs & DNA/LNA chimeras

Deep VentR (exo-) DNA Polymerase  Genetically engineered to eliminate the 3´ → 5´ proofreading exonuclease activity associated with Deep Vent DNA Polymerase  More stable than Vent (exo-) DNA Polymerase - with a half-life of 23 hours at 95°C and 8 hours at 100°C  Both Deep Vent (exo-) & Vent (exo-) DNA Polymerase - suitable for primer extensions - high temperature (72°C) DNA sequencing

Summary of Deep VentR (exo-) DNA Polymerase

Discussion  A Boolean logic NOR gate  Using the surface computing paradigm  One of universal gate in Boolean logic  LNA/DNA chimera  Block polymerase activity & actual computation  LNA: positional preference - in the interaction of the LNA-modified primer & DNA polymerase  MARK & Append-Marked operation - without any modification